Research workbench
Pyruvate phosphate dikinase with bound mg-phosphonopyruvate
Analyse Pyruvate phosphate dikinase with bound mg-phosphonopyruvate in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1KC7
- Type
- protein
- Length
- 872 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pyruvate phosphate dikinase
- EC
- 2.7.9.1
- UniProt
- P22983
- Ligands
- PPR, MG, SO4
- Pockets
- 6 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 50% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pyruvate phosphate dikinase (EC 2.7.9.1) | protein | 872 | 50% helix, 17% strand | P22983 |
Ligands and binding sites
- PPR · Phosphonopyruvate · ligand · chains A
- MG · Magnesium ion · metal · chains A
- SO4 · Sulfate ion · ion · 4 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 843 | 0.83 | 0.85 | 100 | SO4 |
| 2 | 1187 | 0.73 | 0.77 | 117 | empty |
| 3 | 144 | 0.42 | 0.75 | 30 | MG, SO4, PPR |
| 4 | 87 | 0.37 | 0.76 | 18 | empty |
| 5 | 66 | 0.31 | 0.74 | 12 | empty |
Compared structures
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P22983
- Elsewhere: RCSB PDB 1KC7 · PDBe 1KC7 · UniProt P22983
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